Table 1 Validated somatic variants in 1461 human brains

From: Frequency and signature of somatic variants in 1461 human brain exomes

Variant data

Clinical data

Chromosome

Base position

Ref allele

Alt allele

Mutation

Gene

AA change

ExAC

SIFT score

SIFT

Human Proteome expression

Conservation quartile

Methylated in ICM

Exome VAF

Sample ID

Gender

Brain region

Disease group

chr1

248224344

C

T

Non-syn

OR2L3

p.R121C

4.94E-05

0.02

D

Not detected

2

N

15.2%

1

M

Cerebellum

Control

chr7

150815676

C

T

Non-syn

AGAP3

p.S81L

N/A

0.02

D

Expressed in all

4

N

22.3%

2

M

Temporal cortex

Control

chr11

104905100

T

G

Non-syn

CASP1

p.K37Q

4.10E-03

0.59

T

Expressed in all

2

N

16.9%

3

M

Cerebellum

Control

chr17

39502849

T

G

Non-syn

KRT33A

p.R316S

1.10E-03

0.67

T

Not expressed brain

2

N

22.1%

4

M

Cerebellum

CJD

chr3

45837911

T

C

Start lost

SLC6A20

p.M1V

8.77E-05

0.43

T

Not expressed brain

3

N

20.3%

5

M

Cerebellum

Alzheimer disease

chr3

122629742

T

C

Non-syn

SEMA5B

p.H59R

N/A

0.02

D

Elevated brain

4

N

19.3%

5

M

Cerebellum

Alzheimer disease

chr19

36275201

G

A

Non-syn

ARHGAP33

p.A517T

N/A

0.13

T

Mixed expression

3

N

26.0%

6

M

Cerebellum

Other (PSP)

chr12

6138596

C

T

Non-syn

VWF

p.R960P

8.24E-06

0.26

T

Mixed expression

3

N

19.5%

7

F

Cerebellum

Control

chr11

56344581

G

T

Non-syn

OR5M10

p.T206N

1.20E-03

1

T

Not detected

2

N

13.0%

8

F

Cerebellum

Other (epilepsy)

chr16

4833750

A

G

Non-syn

SETP12

p.I131T

1.68E-05

0.01

D

Not expressed brain

1

N

22.8%

9

M

Frontal cortex

Control

chr7

1535876

C

T

Non-syn

INTS1

p.D671N

8.26E-06

0

D

Expressed in all

3

N

14.7%

9

M

Frontal cortex

Control

chr8

144921555

T

C

Non-syn

NRBP2

p.I171V

3.32E-04

0.15

T

Expressed in all

2

N

30.4%

9

M

Frontal cortex

Control

chr2

85991195

C

T

Non-syn

ATOH8

p.R284W

8.30E-06

0

D

Mixed expression

4

Y

28.3%

10

F

Temporal cortex

Control

chr1

24125194

G

A

Non-syn

GALE

p.R50W

1.66E-05

0.02

D

Expressed in all

2

Y

21.7%

11

F

Cerebellum

Control

chr1

17570577

T

C

Non-syn

PADI1

p.C126R

N/A

0.01

D

Not expressed brain

1

N

25.3%

12

M

Cerebellum

Other (dementia)

chr17

76499013

G

A

Syn

DNAH17

N/A

4.05E-03

N/A

N/A

Not expressed brain

N/A

Y

28.2%

12

M

Cerebellum

Other (dementia)

chr11

1718844

T

C

Syn

KRTAP5–6

N/A

1.65E-05

N/A

N/A

Not detected

N/A

N

14.9%

13

F

Cerebellum

FTD-ALS

chr19

9361855

G

A

Non-syn

OR7E24

p.A46T

2.50E-05

0

D

Not expressed brain

1

Y

30.2%

13

F

Cerebellum

FTD-ALS

chr20

60888258

G

A

Syn

LAMA5

N/A

N/A

N/A

N/A

Expressed in all

N/A

N

23.0%

13

F

Cerebellum

FTD-ALS

chr16

88712548

G

A

Syn

CYBA

N/A

N/A

N/A

N/A

Expressed in all

2

Y

23.5%

14

F

Cerebellum

Control

chr22

50752254

G

A

Non-syn

DENND6B

p.R398W

1.66E-05

0

D

Mixed expression

1

Y

20.2%

15

M

Cerebellum

FTD-ALS

chr6

5004177

G

A

Syn

RPP40

N/A

4.12E-05

N/A

N/A

Expressed in all

N/A

N

22.9%

15

M

Cerebellum

FTD-ALS

  1. Variant data shows the chromosome, base position, and reference and alternate allele (hg19 build), together with the amino acid change, frequency in the ExAC population data set,13 SIFT annotation score and classification,24 expression cohort in the Human Proteome Atlas,21 the quartile of genetic conservation within the human genome,13 presence of methylation at that base in the ICM of an early developmental human embryo,18 and the VAF in the exome sequencing (ES) data. Clinical data for each individual comprising sample ID, gender, brain region, and disease group are shown.
  2. AA amino acid, CJD Creutzfeldt–Jakob disease, D deleterious, FTD-ALS frontotemporal dementia–amyotrophic lateral sclerosis, ICM inner cell mass, PD-DLB Parkinson disease–dementia with Lewy bodies, N/A not applicable, Non-syn nonsynonymous, PSP progressive supranuclear palsy, Syn synonymous, T tolerated, VAF variant allele frequency
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